MolNFT v1 · #30963 · protein
Crystal structure of 2-dehydro-3- deoxygluconokinase (ec 2.7.1.45) (TM0067) from thermotoga maritima at 2.05 a resolution
2AFB · 2-keto-3-deoxygluconate kinase: “Crystal structure of 2-dehydro-3- deoxygluconokinase (ec 2.7.1.45) (TM0067) from thermotoga maritima at 2.05…”. X-ray diffraction, 2 ligands (NI, CA), 6 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 2AFB
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-keto-3-deoxygluconate kinase
- Ligands
- NI, CA
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-keto-3-deoxygluconate kinase | protein | 329 | 38% helix, 25% strand | — |
| B | 2-keto-3-deoxygluconate kinase | protein | 326 | 38% helix, 25% strand | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.71 | 0.78 | 70 | empty |
| 2 | 450 | 0.69 | 0.80 | 57 | empty |
| 3 | 146 | 0.41 | 0.74 | 30 | NI |
| 4 | 87 | 0.33 | 0.74 | 19 | NI |
| 5 | 56 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 962 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2AFB · Crystal structure of 2-dehydro-3- deoxygluconokinase (EC 2.7.1.45) (tm0067) from… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2AFB · PDBe 2AFB
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